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windiff - seem to be limited in functionality
winmerge - looks good. free source forge
synchit - costs 30$ 

winmerge 2.x help

These are called filters. These are done through filter files. See the documentation and see how these work.

d:bin
.class
.classpath
.bak

You can navigate to each change and merge them left or right. Similar to eclipse merging capabilities.

http://www.winmerge.org

download the installer

file/open
Pick two directories
You have to navigate into a directory to select
<?xml version="1.0"?>
<project>
        <paths>
                <left>c:\work\project1</left>
                <right>c:\work\project2</right>
                <filter>Visual C++ loose</filter>
                <subfolders>0</subfolders>
        </paths>
</project>

1. Compare directories as indicated above.

2. Pick any filters you want

3. Do open file again.

4. You will see save project

5. Save project into a file

6. Then you can open the project when you need it